rrohwer
commented
1 month ago Hi, I am having this same issue. I ran eukcc on 73 bins, but only 6 appear in the output file. However, in the log I can see that all bins were recognized, and several even had fairly high completeness but were not reported.
This seems like a bug to me.
Thanks, Robin
# the command I used:
eukcc folder --out eukcc_output --threads 20 --db ../eukccdb/eukcc2_db_ver_1.1 --suffix .fna folder_with_73_MAGs
# output file has practically nothing in it
cat eukcc.csv
bin completeness contamination
bin102.fna 0.0 0.0
bin92.fna 7.32 0.0
bin96.fna 0.0 0.0
bin261.fna 10.6 1.0
bin115.fna 1.4 0.0
bin57.fna 3.17 0.0
# but in the log you can see that all 73 bins were found, and some of them were unreported even though they had decent completeness
cat eukcc.log
29-09-2024 14:46:29: EukCC version 2.1.0
29-09-2024 14:46:29: Found 73 bins
29-09-2024 14:56:30: Searching for marker genes in base database
29-09-2024 14:56:31: No placement marker genes found.
29-09-2024 14:56:31: Searching for marker genes in base database
29-09-2024 14:56:31: No placement marker genes found.
29-09-2024 14:56:31: Searching for marker genes in base database
29-09-2024 14:56:31: No placement marker genes found.
29-09-2024 14:56:31: Searching for marker genes in base database
29-09-2024 14:56:31: No placement marker genes found.
29-09-2024 14:56:32: Searching for marker genes in base database
29-09-2024 14:56:33: Found 7 marker genes, placing them in the tree using epa-ng
29-09-2024 14:56:46: Genome belongs to clade: protozoa (Best TaxID: 33846)
29-09-2024 14:56:46: Searching for marker genes in protozoa database
29-09-2024 14:56:47: Found 4 marker genes, placing them in the tree using epa-ng
29-09-2024 14:56:50: Automatically locating best SCMG set
29-09-2024 14:57:17: ❗The choosen marker gene set is supported by only half (1/4) of the alignments. This generally is an unstable estimate.
29-09-2024 14:57:20: Searching fasta for selected markers
29-09-2024 14:57:29: Completeness: 32.74
29-09-2024 14:57:29: Contamination: 3.54
29-09-2024 14:57:29: Max silent contamination: 100.0
29-09-2024 14:57:29: Searching for marker genes in base database
29-09-2024 14:57:29: No placement marker genes found.
29-09-2024 14:57:29: Searching for marker genes in base database
29-09-2024 14:57:29: No placement marker genes found.
29-09-2024 14:57:29: Searching for marker genes in base database
29-09-2024 14:57:31: Found 15 marker genes, placing them in the tree using epa-ng
29-09-2024 14:58:04: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 14:58:04: Searching for marker genes in protozoa database
29-09-2024 14:58:06: Found 22 marker genes, placing them in the tree using epa-ng
29-09-2024 14:58:30: Automatically locating best SCMG set
29-09-2024 14:59:02: ❗The choosen marker gene set is supported by only half (9/22) of the alignments. This generally is an unstable estimate.
29-09-2024 14:59:02: Searching fasta for selected markers
29-09-2024 14:59:05: Completeness: 41.18
29-09-2024 14:59:05: Contamination: 11.76
29-09-2024 14:59:05: Max silent contamination: 100.0
29-09-2024 14:59:05: Searching for marker genes in base database
29-09-2024 14:59:06: No placement marker genes found.
29-09-2024 14:59:06: Searching for marker genes in base database
29-09-2024 14:59:06: Found 8 marker genes, placing them in the tree using epa-ng
29-09-2024 14:59:17: Genome belongs to clade: protozoa (Best TaxID: 6020)
29-09-2024 14:59:17: Searching for marker genes in protozoa database
29-09-2024 14:59:18: Found 6 marker genes, placing them in the tree using epa-ng
29-09-2024 14:59:21: Automatically locating best SCMG set
29-09-2024 14:59:42: ❗The choosen marker gene set is supported by only half (2/6) of the alignments. This generally is an unstable estimate.
29-09-2024 14:59:43: Searching fasta for selected markers
29-09-2024 14:59:44: Completeness: 31.17
29-09-2024 14:59:44: Contamination: 0.0
29-09-2024 14:59:44: Max silent contamination: 100.0
29-09-2024 14:59:44: Searching for marker genes in base database
29-09-2024 14:59:45: No placement marker genes found.
29-09-2024 14:59:45: Searching for marker genes in base database
29-09-2024 14:59:45: No placement marker genes found.
29-09-2024 14:59:45: Searching for marker genes in base database
29-09-2024 14:59:46: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 14:59:50: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 14:59:50: Searching for marker genes in protozoa database
29-09-2024 14:59:50: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 14:59:53: Automatically locating best SCMG set
29-09-2024 15:00:21: Searching fasta for selected markers
29-09-2024 15:00:21: Completeness: 0.0
29-09-2024 15:00:21: Contamination: 0.0
29-09-2024 15:00:21: Max silent contamination: 100.0
29-09-2024 15:00:21: Searching for marker genes in base database
29-09-2024 15:00:22: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:00:26: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 15:00:26: Searching for marker genes in protozoa database
29-09-2024 15:00:27: No placement marker genes found.
29-09-2024 15:00:27: Searching for marker genes in base database
29-09-2024 15:00:27: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:00:30: Genome belongs to clade: protozoa (Best TaxID: 174815)
29-09-2024 15:00:30: Searching for marker genes in protozoa database
29-09-2024 15:00:31: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:00:33: Automatically locating best SCMG set
29-09-2024 15:00:56: Searching fasta for selected markers
29-09-2024 15:00:56: Completeness: 7.32
29-09-2024 15:00:56: Contamination: 0.0
29-09-2024 15:00:56: Max silent contamination: 100.0
29-09-2024 15:00:56: Searching for marker genes in base database
29-09-2024 15:00:56: No placement marker genes found.
29-09-2024 15:00:56: Searching for marker genes in base database
29-09-2024 15:00:57: No placement marker genes found.
29-09-2024 15:00:57: Searching for marker genes in base database
29-09-2024 15:00:57: Found 3 marker genes, placing them in the tree using epa-ng
29-09-2024 15:01:02: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 15:01:02: Searching for marker genes in protozoa database
29-09-2024 15:01:02: No placement marker genes found.
29-09-2024 15:01:02: Searching for marker genes in base database
29-09-2024 15:01:03: No placement marker genes found.
29-09-2024 15:01:03: Searching for marker genes in base database
29-09-2024 15:01:03: No placement marker genes found.
29-09-2024 15:01:03: Searching for marker genes in base database
29-09-2024 15:01:03: Found 10 marker genes, placing them in the tree using epa-ng
29-09-2024 15:01:16: Genome belongs to clade: protozoa (Best TaxID: 5878)
29-09-2024 15:01:16: Searching for marker genes in protozoa database
29-09-2024 15:01:17: Found 6 marker genes, placing them in the tree using epa-ng
29-09-2024 15:01:21: Automatically locating best SCMG set
29-09-2024 15:01:42: ❗The choosen marker gene set is supported by only half (2/6) of the alignments. This generally is an unstable estimate.
29-09-2024 15:01:43: Searching fasta for selected markers
29-09-2024 15:01:45: Completeness: 31.17
29-09-2024 15:01:45: Contamination: 6.49
29-09-2024 15:01:45: Max silent contamination: 100.0
29-09-2024 15:01:45: Searching for marker genes in base database
29-09-2024 15:01:45: No placement marker genes found.
29-09-2024 15:01:45: Searching for marker genes in base database
29-09-2024 15:01:45: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:01:49: Genome belongs to clade: protozoa (Best TaxID: 5654)
29-09-2024 15:01:49: Searching for marker genes in protozoa database
29-09-2024 15:01:50: No placement marker genes found.
29-09-2024 15:01:50: Searching for marker genes in base database
29-09-2024 15:01:50: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:01:53: Genome belongs to clade: protozoa (Best TaxID: 2699528)
29-09-2024 15:01:53: Searching for marker genes in protozoa database
29-09-2024 15:01:53: No placement marker genes found.
29-09-2024 15:01:53: Searching for marker genes in base database
29-09-2024 15:01:54: No placement marker genes found.
29-09-2024 15:01:54: Searching for marker genes in base database
29-09-2024 15:01:54: No placement marker genes found.
29-09-2024 15:01:54: Searching for marker genes in base database
29-09-2024 15:01:54: No placement marker genes found.
29-09-2024 15:01:54: Searching for marker genes in base database
29-09-2024 15:01:55: No placement marker genes found.
29-09-2024 15:01:55: Searching for marker genes in base database
29-09-2024 15:01:55: No placement marker genes found.
29-09-2024 15:01:55: Searching for marker genes in base database
29-09-2024 15:01:55: No placement marker genes found.
29-09-2024 15:01:55: Searching for marker genes in base database
29-09-2024 15:01:55: No placement marker genes found.
29-09-2024 15:01:55: Searching for marker genes in base database
29-09-2024 15:01:56: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:02:00: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 15:02:00: Searching for marker genes in protozoa database
29-09-2024 15:02:01: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:02:04: Automatically locating best SCMG set
29-09-2024 15:02:31: Searching fasta for selected markers
29-09-2024 15:02:32: Completeness: 0.0
29-09-2024 15:02:32: Contamination: 0.0
29-09-2024 15:02:32: Max silent contamination: 100.0
29-09-2024 15:02:32: Searching for marker genes in base database
29-09-2024 15:02:32: No placement marker genes found.
29-09-2024 15:02:32: Searching for marker genes in base database
29-09-2024 15:02:32: No placement marker genes found.
29-09-2024 15:02:32: Searching for marker genes in base database
29-09-2024 15:02:33: Found 3 marker genes, placing them in the tree using epa-ng
29-09-2024 15:02:37: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 15:02:37: Searching for marker genes in protozoa database
29-09-2024 15:02:38: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:02:41: Automatically locating best SCMG set
29-09-2024 15:03:17: Searching fasta for selected markers
29-09-2024 15:03:25: Completeness: 10.6
29-09-2024 15:03:25: Contamination: 1.0
29-09-2024 15:03:25: Max silent contamination: 100.0
29-09-2024 15:03:25: Searching for marker genes in base database
29-09-2024 15:03:26: Found 4 marker genes, placing them in the tree using epa-ng
29-09-2024 15:03:32: Genome belongs to clade: protozoa (Best TaxID: 33634)
29-09-2024 15:03:32: Searching for marker genes in protozoa database
29-09-2024 15:03:32: Found 5 marker genes, placing them in the tree using epa-ng
29-09-2024 15:03:35: Automatically locating best SCMG set
29-09-2024 15:04:02: ❗The choosen marker gene set is supported by only half (1/5) of the alignments. This generally is an unstable estimate.
29-09-2024 15:04:06: Searching fasta for selected markers
29-09-2024 15:04:09: Completeness: 25.58
29-09-2024 15:04:09: Contamination: 10.23
29-09-2024 15:04:09: Max silent contamination: 100.0
29-09-2024 15:04:09: Searching for marker genes in base database
29-09-2024 15:04:09: No placement marker genes found.
29-09-2024 15:04:09: Searching for marker genes in base database
29-09-2024 15:04:10: No placement marker genes found.
29-09-2024 15:04:10: Searching for marker genes in base database
29-09-2024 15:04:10: No placement marker genes found.
29-09-2024 15:04:10: Searching for marker genes in base database
29-09-2024 15:04:10: No placement marker genes found.
29-09-2024 15:04:10: Searching for marker genes in base database
29-09-2024 15:04:11: Found 11 marker genes, placing them in the tree using epa-ng
29-09-2024 15:04:33: Genome belongs to clade: protozoa (Best TaxID: 33846)
29-09-2024 15:04:33: Searching for marker genes in protozoa database
29-09-2024 15:04:34: Found 8 marker genes, placing them in the tree using epa-ng
29-09-2024 15:04:42: Automatically locating best SCMG set
29-09-2024 15:05:08: ❗The choosen marker gene set is supported by only half (1/8) of the alignments. This generally is an unstable estimate.
29-09-2024 15:05:12: Searching fasta for selected markers
29-09-2024 15:05:20: Completeness: 29.2
29-09-2024 15:05:20: Contamination: 0.88
29-09-2024 15:05:20: Max silent contamination: 100.0
29-09-2024 15:05:20: Searching for marker genes in base database
29-09-2024 15:05:21: Found 14 marker genes, placing them in the tree using epa-ng
29-09-2024 15:05:50: Genome belongs to clade: protozoa (Best TaxID: 33846)
29-09-2024 15:05:50: Searching for marker genes in protozoa database
29-09-2024 15:05:52: Found 11 marker genes, placing them in the tree using epa-ng
29-09-2024 15:06:01: Automatically locating best SCMG set
29-09-2024 15:06:28: ❗The choosen marker gene set is supported by only half (1/11) of the alignments. This generally is an unstable estimate.
29-09-2024 15:06:32: Searching fasta for selected markers
29-09-2024 15:06:42: Completeness: 48.67
29-09-2024 15:06:42: Contamination: 2.65
29-09-2024 15:06:42: Max silent contamination: 100.0
29-09-2024 15:06:42: Searching for marker genes in base database
29-09-2024 15:06:42: No placement marker genes found.
29-09-2024 15:06:42: Searching for marker genes in base database
29-09-2024 15:06:43: No placement marker genes found.
29-09-2024 15:06:43: Searching for marker genes in base database
29-09-2024 15:06:43: No placement marker genes found.
29-09-2024 15:06:43: Searching for marker genes in base database
29-09-2024 15:06:43: No placement marker genes found.
29-09-2024 15:06:43: Searching for marker genes in base database
29-09-2024 15:06:44: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:06:47: Genome belongs to clade: protozoa (Best TaxID: 37358)
29-09-2024 15:06:47: Searching for marker genes in protozoa database
29-09-2024 15:06:48: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:06:50: Automatically locating best SCMG set
29-09-2024 15:07:17: Could not identify a single suitable marker gene set
29-09-2024 15:07:17: No marker gene set could be found with these settings 🙁
Change your parameters and try again?
29-09-2024 15:07:17: Searching for marker genes in base database
29-09-2024 15:07:17: No placement marker genes found.
29-09-2024 15:07:17: Searching for marker genes in base database
29-09-2024 15:07:17: No placement marker genes found.
29-09-2024 15:07:17: Searching for marker genes in base database
29-09-2024 15:07:18: No placement marker genes found.
29-09-2024 15:07:18: Searching for marker genes in base database
29-09-2024 15:07:18: No placement marker genes found.
29-09-2024 15:07:18: Searching for marker genes in base database
29-09-2024 15:07:19: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:07:24: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 15:07:24: Searching for marker genes in protozoa database
29-09-2024 15:07:25: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:07:28: Automatically locating best SCMG set
29-09-2024 15:07:55: Could not identify a single suitable marker gene set
29-09-2024 15:07:55: No marker gene set could be found with these settings 🙁
Change your parameters and try again?
29-09-2024 15:07:55: Searching for marker genes in base database
29-09-2024 15:07:55: No placement marker genes found.
29-09-2024 15:07:55: Searching for marker genes in base database
29-09-2024 15:07:55: No placement marker genes found.
29-09-2024 15:07:55: Searching for marker genes in base database
29-09-2024 15:07:55: No placement marker genes found.
29-09-2024 15:07:55: Searching for marker genes in base database
29-09-2024 15:07:56: Found 5 marker genes, placing them in the tree using epa-ng
29-09-2024 15:08:04: Genome belongs to clade: protozoa (Best TaxID: 33634)
29-09-2024 15:08:04: Searching for marker genes in protozoa database
29-09-2024 15:08:05: Found 3 marker genes, placing them in the tree using epa-ng
29-09-2024 15:08:08: Automatically locating best SCMG set
29-09-2024 15:08:46: ❗The choosen marker gene set is supported by only half (1/3) of the alignments. This generally is an unstable estimate.
29-09-2024 15:08:57: Searching fasta for selected markers
29-09-2024 15:09:10: Completeness: 2.0
29-09-2024 15:09:10: Contamination: 0.4
29-09-2024 15:09:10: Max silent contamination: 100.0
29-09-2024 15:09:10: Searching for marker genes in base database
29-09-2024 15:09:10: No placement marker genes found.
29-09-2024 15:09:10: Searching for marker genes in base database
29-09-2024 15:09:11: Found 4 marker genes, placing them in the tree using epa-ng
29-09-2024 15:09:18: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 15:09:18: Searching for marker genes in protozoa database
29-09-2024 15:09:18: Found 5 marker genes, placing them in the tree using epa-ng
29-09-2024 15:09:22: Automatically locating best SCMG set
29-09-2024 15:09:43: ❗The choosen marker gene set is supported by only half (2/5) of the alignments. This generally is an unstable estimate.
29-09-2024 15:09:44: Searching fasta for selected markers
29-09-2024 15:09:45: Completeness: 25.97
29-09-2024 15:09:45: Contamination: 1.3
29-09-2024 15:09:45: Max silent contamination: 100.0
29-09-2024 15:09:45: Searching for marker genes in base database
29-09-2024 15:09:46: No placement marker genes found.
29-09-2024 15:09:46: Searching for marker genes in base database
29-09-2024 15:09:46: No placement marker genes found.
29-09-2024 15:09:46: Searching for marker genes in base database
29-09-2024 15:09:47: Found 7 marker genes, placing them in the tree using epa-ng
29-09-2024 15:10:00: Genome belongs to clade: protozoa (Best TaxID: 33630)
29-09-2024 15:10:00: Searching for marker genes in protozoa database
29-09-2024 15:10:01: Found 11 marker genes, placing them in the tree using epa-ng
29-09-2024 15:10:12: Automatically locating best SCMG set
29-09-2024 15:10:48: ❗The choosen marker gene set is supported by only half (4/11) of the alignments. This generally is an unstable estimate.
29-09-2024 15:10:55: Searching fasta for selected markers
29-09-2024 15:11:11: Completeness: 48.38
29-09-2024 15:11:11: Contamination: 4.86
29-09-2024 15:11:11: Max silent contamination: 100.0
29-09-2024 15:11:11: Searching for marker genes in base database
29-09-2024 15:11:12: No placement marker genes found.
29-09-2024 15:11:12: Searching for marker genes in base database
29-09-2024 15:11:12: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:11:15: Genome belongs to clade: protozoa (Best TaxID: 31345)
29-09-2024 15:11:15: Searching for marker genes in protozoa database
29-09-2024 15:11:15: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:11:17: Automatically locating best SCMG set
29-09-2024 15:11:53: Searching fasta for selected markers
29-09-2024 15:11:57: Completeness: 1.4
29-09-2024 15:11:57: Contamination: 0.0
29-09-2024 15:11:57: Max silent contamination: 100.0
29-09-2024 15:11:57: Searching for marker genes in base database
29-09-2024 15:11:58: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:12:01: Genome belongs to clade: protozoa (Best TaxID: 1242273)
29-09-2024 15:12:01: Searching for marker genes in protozoa database
29-09-2024 15:12:01: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:12:03: Automatically locating best SCMG set
29-09-2024 15:12:30: Could not identify a single suitable marker gene set
29-09-2024 15:12:30: No marker gene set could be found with these settings 🙁
Change your parameters and try again?
29-09-2024 15:12:30: Searching for marker genes in base database
29-09-2024 15:12:30: No placement marker genes found.
29-09-2024 15:12:30: Searching for marker genes in base database
29-09-2024 15:12:31: Found 9 marker genes, placing them in the tree using epa-ng
29-09-2024 15:12:42: Genome belongs to clade: protozoa (Best TaxID: 5878)
29-09-2024 15:12:42: Searching for marker genes in protozoa database
29-09-2024 15:12:43: Found 10 marker genes, placing them in the tree using epa-ng
29-09-2024 15:12:47: Automatically locating best SCMG set
29-09-2024 15:13:16: ❗The choosen marker gene set is supported by only half (4/10) of the alignments. This generally is an unstable estimate.
29-09-2024 15:13:19: Searching fasta for selected markers
29-09-2024 15:13:23: Completeness: 33.02
29-09-2024 15:13:23: Contamination: 11.16
29-09-2024 15:13:23: Max silent contamination: 100.0
29-09-2024 15:13:23: Searching for marker genes in base database
29-09-2024 15:13:24: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:13:28: Genome belongs to clade: protozoa (Best TaxID: 5738)
29-09-2024 15:13:28: Searching for marker genes in protozoa database
29-09-2024 15:13:28: Found 2 marker genes, placing them in the tree using epa-ng
29-09-2024 15:13:31: Automatically locating best SCMG set
29-09-2024 15:13:47: Searching fasta for selected markers
29-09-2024 15:13:47: Completeness: 3.17
29-09-2024 15:13:47: Contamination: 0.0
29-09-2024 15:13:47: Max silent contamination: 100.0
29-09-2024 15:13:47: Searching for marker genes in base database
29-09-2024 15:13:48: Found 9 marker genes, placing them in the tree using epa-ng
29-09-2024 15:14:07: Genome belongs to clade: protozoa (Best TaxID: 33846)
29-09-2024 15:14:07: Searching for marker genes in protozoa database
29-09-2024 15:14:08: Found 6 marker genes, placing them in the tree using epa-ng
29-09-2024 15:14:14: Automatically locating best SCMG set
29-09-2024 15:14:41: Could not identify a single suitable marker gene set
29-09-2024 15:14:41: No marker gene set could be found with these settings 🙁
Change your parameters and try again?
29-09-2024 15:14:41: Searching for marker genes in base database
29-09-2024 15:14:41: No placement marker genes found.
29-09-2024 15:14:41: Searching for marker genes in base database
29-09-2024 15:14:41: No placement marker genes found.
29-09-2024 15:14:41: Searching for marker genes in base database
29-09-2024 15:14:41: Found 1 marker genes, placing them in the tree using epa-ng
29-09-2024 15:14:45: Genome belongs to clade: protozoa (Best TaxID: 2699528)
29-09-2024 15:14:45: Searching for marker genes in protozoa database
29-09-2024 15:14:45: No placement marker genes found.
29-09-2024 15:14:45: Searching for marker genes in base database
29-09-2024 15:14:45: No placement marker genes found.
29-09-2024 15:14:45: Searching for marker genes in base database
29-09-2024 15:14:46: Found 3 marker genes, placing them in the tree using epa-ng
29-09-2024 15:14:51: Genome belongs to clade: protozoa (Best TaxID: protist_common)
29-09-2024 15:14:51: Searching for marker genes in protozoa database
29-09-2024 15:14:52: Found 4 marker genes, placing them in the tree using epa-ng
29-09-2024 15:14:55: Automatically locating best SCMG set
29-09-2024 15:15:22: ❗The choosen marker gene set is supported by only half (1/4) of the alignments. This generally is an unstable estimate.
29-09-2024 15:15:26: Searching fasta for selected markers
29-09-2024 15:15:29: Completeness: 6.64
29-09-2024 15:15:29: Contamination: 0.44
29-09-2024 15:15:29: Max silent contamination: 100.0
29-09-2024 15:15:29: Found 0 large bins to merge with
29-09-2024 15:15:29: Created 0 merged bins
Hi,
I have several bins (say 1.faa 2.faa ... 100.faa) in a bin/ folder. In single mode, EukCC successfully gave results for ~ 70% of them. However, when in folder mode, some of the bins were lost from the eukcc.csv file. Is there a reason for that?
Also, the folder mode merged two bins together, even though I did not provide the link table. Would this be a bug or an expected behavior?
Thanks! Jing